Your first two and last sentences contradict each other.
But do you know whether 50 minutes of non-stop over-unders is actually a good idea? If you look at how TR workouts do over-unders, they are usually broken down in 12-20 minute sets with 3-6 minute breaks in between. You need the breaks to really nail the intervals, otherwise you are not doing over-unders, but rather under-unders 
So already here I would say you are leaving something on the table, and the outdoor interval is less efficient.
Auto pause is on by default, so unless you have disabled it, you are using it. Stops at intersections and traffic lights are thusly not counted.
The amount of coasting depends on your environment and on your pacing strategy. Perhaps it makes little sense to pedal like crazy in order to eek out the last 5 km/h on a descent. Instead, you’d use that time strategically to give your legs some rest so that you can power up the next short hill at VO2max or some such. Even during my races, I typically spend 10-20 % coasting, “doing nothing” 
But those are things to train, which are complementary to what you do on a trainer.
I think you are conflating different types of training. Yes, if you are racing down a single track, your upper body does plenty of work. That can — and should be — part of your training. But this is complementary to being on an indoor trainer, and can’t really be compared with one another.